I suppose this is a editorial nightmare. I think that multiple timelines can be a ball of yarn that twists and turns so that eventually a ending is accepted in the 616 X-men U, that is apart of the greater 616 or post Secret Wars.
I think that any interaction with a alternate timeline or future timeline can be undone by certain events being altered.
Now the question is how would you streamline the future X-men timeline ala Jim Shooter style to settle the shifting sands of the timeline?
I wonder could some Alt- timeline, Timehopping X-men that have had interactions with the X-men like Rachel Grey, Bishop, and others could influence things that may cause similarities in their futures to occur under different circumstances.
So basically try to connect the future timelines to make less of a clutter of the X-men timeline.